Question: Should genus and species be specified when annotating de novo assemblies using Prokka
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gravatar for Kong2008
2.4 years ago by
Kong20080
Kong20080 wrote:

Hi everyone, Could you please advise me whether genus and species should be specified when annotating my assemblie with Prokka and RAST. I've just started learning genomics, bioinformatics and I'm working in genomics of Nocardia nova whose reference genomes are available. I have sequenced whole genomes of some samples. few of them are Nocardia nova and the rest are Nocardia sp. I did de novo assembling using Spades and now I want to do annotation for these de novo assemblies using the command below.

prokka input AAAA_contigs.fasta file --outdir AAAA --prefix AAAA --kingdom Bacteria --gcode 11 --genus Nocardia --species nova --locustag AAAA --addgenes

My questions: 1. Does the command look good and in the Prokka manual, gcode is defined as Genetic code / Translation table, is 11 the code of Bacteria? 2. I wonder whether if the details of genus, species are designated for annotation tools such as Prokka, RAST, then these tools would only annotate my assemblies against databases of this particular species, so they might give biased results towards the databases of reference genomes. What do you think ?

  1. I did annotation using the command below.
    prokka input AAAA_contigs.fasta file --outdir AAAA --prefix AAAA --locustag AAAA --addgenes

But can't open gff file in Artemis, Artermis reported errors "CDS can't have product=hypothetical as a qualifier-ignore error and continue", "aborted - too many errors while reading: the AAAA.gff".

Thank you so much for any helps and suggetion!

assembly genome • 1.1k views
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